Cold-pressed oils are highly prone to the peroxidation process, which causes a rapid decline in quality. Thus, there is a need to develop instrumental methods instead of conventional chemical analysis consuming large quantities of harmful chemicals. Differential scanning calorimetry (DSC) is a valuable analytical tool for assessing the oxidative stability of oils. Cold-pressed flaxseed, camelina and hemp seed oils from different cultivars, which had been stored for six months in room conditions under natural light exposure, were tested. Chemical methods for measuring changes in oxidative stability during storage of oils included determination of peroxide value (PV), p-Anisidine value (p-AV), total oxidation value (TOTOX) value and acid value (AV). Parameters like oxidation induction time (OIT) in isothermal mode (120, 140 °C) and onset temperature (Ton) in non-isothermal mode (heating rate 2, 5 °C/min) were established from DSC curves. Data for OIT and Ton plotted against time showed a strong, significant (p ≤ 0.05) descending trend for all oils. However, flaxseed and hempseed oils revealed a more rapid deterioration during storage compared to camelina seed oils. All DSC results showed promising repeatability of the oxidative characteristics for three types of cold-pressed oils, regardless of their origins in different cultivars. However, the most suitable for monitoring the deteriorative changes in oils during storage was the isothermal test carried out at a temperature of 120 °C, for which the correlations with chemical indicators (PV, p-AV, TOTOX) were highly significant (p ≤ 0.0001). Linear discriminant analysis (LDA) based on the DSC results revealed, that the first discriminating function significantly separated the fresh oils from stored oils. The study showed that, based on a starting point defined for fresh oils, the DSC technique can be used to effectively and ecologically monitor the deterioration of oils by oxidation, instead of harmful chemical analyses.